Another hypothesis is that it isn't matter that's causing the observed phenomena but some other macro phenomenon, or that the common model is flawed.

Kepler's Laws, Relativity, Quantum Mechanics, Newtonian Mechanics, everything since the time of Copernicus gets tossed out? Go back to Ptolemy and his epicycles? That is the implication of the standard model being wrong by this order of magnitude and it isn't something to be done casually.

Second, if the calculations only make sense if there is more matter than we can currently observe it follows, by the logic of the law of excluded middle, that either the standard model is false or that there is matter that we cannot currently observe (i.e. dark matter). Logically, there is no, and cannot be a, third option.

No third option if and only if the framework used for the calculations actually reflects underlying reality. What if something else, not in the current model, is producing the effects attributed to dark matter and dark energy?

Yes, which was my point exactly: "…either the standard model is false or…"

_________________Καὶ ὁ λόγος σὰρξ ἐγένετο

“Being religious means asking passionately the question of the meaning of our existence and being willing to receive answers, even if the answers hurt.” — Paul Tillich

I think it safe to say that while we cannot claim demonstrative certitude of dark matter or many elements of the standard theory, it would be unreasonable, with the state of the evidence, to treat it as merely one hypothesis among many. We are warranted in treating the standard model as true, and quite unwarranted in the contrary. Even though we admit that there could be some error. Hence, we can say it is more than an hypothesis, a suspicion, but a justified opinion, and its contrary is not. And by opinion I mean where the mind is wholly assenting to one side of a contradiction, though with the possibility of error (however slight) being admitted.

Or perhaps you missed the point of his post, which I took to be a comparison of aether (a discarded theory) with dark matter, not an attempt to say that aether is the same thing as dark matter.

The implications of rejecting the aether are far less consequential than the implications of throwing out something as basic and fundamental as Kepler's laws. However, the example of the luminiferous aether is an illustrative example, because before that theory was abandoned, every possible attempt to save the theory was made, it was thrown out only when every possible attempt to preserve the theory failed and it became clear that there was simply nowhere else to go.

There is no way to throw out something as fundamental as Kepler's Laws without also throwing out everything that depends on it, which is just about all of modern astronomy. I'm not saying that we should regard Kepler's Laws as a kind of dogma that can never be questioned, however, to just casually say 'well, I think we should just decide that everything we think we have learned about the cosmos for the last 500 years is wrong', is extremely short-sighted. You don't do something that extreme except as a desperate, last-ditch measure when everything else has failed. We are we are nowhere near that point yet, and until we are at that point, talking about 'throwing out the common model' is extremely premature.

What other 'hypothesis' possibly there be? Either there is enough matter in the universe to make the equations work, or there isn't. There is no third option.

As I said, I've read some on this and every time I do it's like the more I read the furtherer behind I get, so I'm certainly not anyone to look to for great expectations. It does feel like we're trying to put 10# of dirt in a 5# bag when we don't even know what the dirt is and the bag is seemingly ok in galactic proportions but seriously lacking in universal, meaning we really aren't too sure about the bag either. We can never throw out the baby with the bath water in regards to previous findings, heck all our findings in all we have ever done are formulated on something we'd done / learned previously. But there is something missing here and it will some day be resolved by either new hypothesis of current knowledge or another option that is here-to-fore completely unknown to us, but in our face our entire existence.

Don't be upset because I missed on the 20 years back in dark matter knowledge. I only went back as far as I could remember it in science. That's not really the point I was trying to make. The point is I am uncomfortable with a lack of possibility that there's something new a foot here and one way or another, the final answer will effect the physical application of E=MC2. You seem to have a much better handle on this, but I can't allow for the totally unexpected to happen, just, as I expect the detractors of Christ became aware He did rebuild the Temple in 3 days in an all together new fashion from there thinking.

_________________The truth of the Real Presence "cannot be apprehended by the senses but only by faith which relies on divine authority" (St. Thomas Aquinas)

_________________'The only cure for sagging or fainting faith is Communion.... Like the act of Faith it must be continuous and grow by exercise. Frequency is of the highest effect. Seven times a week is more nourishing than seven times at intervals.' J.R.R. Tolkien